User:Tilman Schirmer/Sandbox 99
From Proteopedia
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The <scene name='User:Tilman_Schirmer/Sandbox_99/Diala/20'>peptide bond </scene> formation is a condensation reaction between the carboxyl group of the amino acid n<sub>i</sub> and the amino group of the amino acid n<sub>i+1</sub>. | The <scene name='User:Tilman_Schirmer/Sandbox_99/Diala/20'>peptide bond </scene> formation is a condensation reaction between the carboxyl group of the amino acid n<sub>i</sub> and the amino group of the amino acid n<sub>i+1</sub>. | ||
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| + | The peptide bond is a resonance structure between two limiting states. Therefore the N-C bond has a partial double bond character and the atoms/groups C<sub>α</sub>, HN, C, C=O are within one plane. Peptide bonds are usually in trans conformation (ω torsion angle= 180°) due to sterical hindrance between C<sub>β</sub> and the C=O carbonyl. Cis conformation can occur only for the peptide bonds preceding Pro or Gly residue, where no C<sub>β</sub> is interfering. | ||
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| + | If the three torsion angles phi, psi and omega of every amino acids within a protein are known, the secondary structure of this protein can approximated (?). | ||
The <scene name='User:Tilman_Schirmer/Sandbox_99/Phi_angle/2'>Phi torsion angle</scene> is defined by the four atoms φ = C - N - C<sub>α</sub> - C (yellow: bond between N - C<sub>α</sub>). | The <scene name='User:Tilman_Schirmer/Sandbox_99/Phi_angle/2'>Phi torsion angle</scene> is defined by the four atoms φ = C - N - C<sub>α</sub> - C (yellow: bond between N - C<sub>α</sub>). | ||
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The <scene name='User:Tilman_Schirmer/Sandbox_99/Omega_angle/7'>Omega torsion angle</scene> is defined by the four atoms ω = C<sub>α</sub> - C - N - C<sub>α</sub> (orange: bond between C - N). | The <scene name='User:Tilman_Schirmer/Sandbox_99/Omega_angle/7'>Omega torsion angle</scene> is defined by the four atoms ω = C<sub>α</sub> - C - N - C<sub>α</sub> (orange: bond between C - N). | ||
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| - | The peptide bond is a resonance structure between two limiting states. Therefore the N-C bond has a partial double bond character and the atoms/groups C<sub>α</sub>, HN, C, C=O are within one plane. Peptide bonds are usually in trans conformation (ω torsion angle= 180°) due to sterical hindrance between C<sub>β</sub> and the C=O carbonyl. Cis conformation can occur only for the peptide bonds preceding Pro or Gly residue, where no C<sub>β</sub> is interfering. | ||
Revision as of 16:56, 25 February 2010
Peptide bond
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The formation is a condensation reaction between the carboxyl group of the amino acid ni and the amino group of the amino acid ni+1.
The peptide bond is a resonance structure between two limiting states. Therefore the N-C bond has a partial double bond character and the atoms/groups Cα, HN, C, C=O are within one plane. Peptide bonds are usually in trans conformation (ω torsion angle= 180°) due to sterical hindrance between Cβ and the C=O carbonyl. Cis conformation can occur only for the peptide bonds preceding Pro or Gly residue, where no Cβ is interfering.
If the three torsion angles phi, psi and omega of every amino acids within a protein are known, the secondary structure of this protein can approximated (?).
The is defined by the four atoms φ = C - N - Cα - C (yellow: bond between N - Cα).
The is defined by the four atoms ψ = N - Cα - C - N (green: bond between Cα - C).
The is defined by the four atoms ω = Cα - C - N - Cα (orange: bond between C - N).
